Civil society is an essential component of any democracy and it will be a key factor in determining the success of the democratic transitions now underway in the Middle East and North Africa. In his May 19 speech, President Barack Obama identified “a vibrant civil society” as one of four areas in which Egypt and Tunisia should set a strong example for the region. Speaking to a global forum in Sweden last month, Secretary Hillary Clinton described civil society as “a force for progress around the world,” while noting that “in too many places, governments are treating civil society activists as adversaries, rather than partners.” Sadly, nowhere is that now more true than in Egypt, where the ruling Supreme Council of the Armed Forces (SCAF) has steadily escalated a campaign against this community which is even more repressive than during the Mubarak era.

Unlike neighboring Libya and Tunisia, in which civil society was almost nonexistent prior to the revolutions of this year, Egypt has thousands of longstanding civil society organizations. Under Mubarak, the vast majority of these groups avoided any political issues, human rights concerns, or criticism of the Mubarak regime, instead focusing on issues such as health, education, and family welfare. The small subset of these groups that dared to work on political issues or human rights abuses were often the target of government harassment, interference, and intimidation. In the weeks following Mubarak’s fall, Egyptian NGOs were eager to play a broader role and to help guide the political processes during Egypt’s transition. Unfortunately, frustration set in quickly as the SCAF appeared to entirely ignore the views of civil society in its decision-making process. Tensions grew throughout the spring as the SCAF continued to ignore the demands and recommendations of civil society actors and increasingly sought to undermine their reputation with the Egyptian public, primarily through stories in the state-run media implying that Egyptian NGOs are working on behalf of foreign agendas.

In recent months, the SCAF has dramatically escalated these attacks on civil society. On July 12, Minister of International Cooperation Faiza Abul-Naga announced that the government would establish a commission of inquiry to investigate the funding of civil society organizations. Only two weeks later, state-owned October magazine ran a cover story — illustrated with a crude depiction of U.S. Ambassador to Egypt Anne Patterson burning Tahrir Square with flaming U.S. dollars — that accused the United States of undermining Egypt’s revolution by funding civil society organizations.

The most recent and alarming step in the SCAF’s assault was revealed in a September 26 article in Al-Fagr newspaper summarizing the results of the government’s investigation. The report not only detailed the amounts of funding received by numerous NGOs but also declared 39 organizations to be “illegal.” This followed reports in official newspapers in August that some of the NGOs under investigation would be charged with high treason and undermining national security on behalf of “foreign agendas,” charges punishable by up to 15 years in prison.

The list of so-called “illegal” NGOs include many of Egypt’s oldest and most respected human rights organizations such as the Cairo Institute for Human Rights Studies, the El-Nadeem Center for Rehabilitation of Victims of Torture, the Egyptian Initiative for Personal Rights, and the Hisham Mubarak Law Center. The list also includes three Washington-based organizations that work to support democracy worldwide: the National Democratic Institute (NDI), the International Republican Institute (IRI), and Freedom House.

These groups are now suddenly being classified as “illegal” on the grounds that they are not officially registered under Egypt’s existing, restrictive NGO law 84/2002, which extends wide-reaching authority to the Ministry of Social Solidarity to control the activities, funding, and board membership of NGOs as well as to dissolve NGOs when deemed appropriate. Many of the “unregistered” NGOs are in fact legally registered entities in Egypt, but they are registered as civil corporations, law firms, or other legal entities that are supervised by less intrusive government ministries and laws. Although hundreds of Egyptian organizations are not officially registered under law 84/2002, it appears that the specific 39 declared illegal have been targeted because of their focus on democracy and human rights. During the Mubarak era, the Egyptian government often interfered with the work of these “unregistered” organizations, but it never went so far as to declare dozens of NGOs to be illegal and threaten to charge them with serious crimes on the basis of their registration status. Following Egypt’s historic protests calling for basic political freedoms, it is deeply disturbing that the Egyptian military has targeted Egypt’s democracy and human rights community in ways not even dared during Mubarak’s despotic rule.

There is also tragic irony in the Egyptian military attacking human rights organizations for receiving foreign funding, when by far the largest recipient of foreign funding in Egypt is the military, itself. The headline in Al-Fagr this week declared that $225 million has been distributed to Egyptian organizations by the United States, Europe, and the Gulf countries since Mubarak’s fall. But this amount pales in comparison to the $1.3 billion that the Egyptian military has received from the United States annually for decades. If the acceptance of foreign funds implied working to undermine Egypt on behalf of foreign interests, then the Egyptian military would be the guiltiest party of such crimes.

The $1.3 billion in annual military aid — nearly 30 percent of the Egyptian military’s budget — should, in theory, give the United States significant leverage in its relationship with the SCAF. Although successive U.S. administrations have been loath to use military aid in this way, the SCAF should know that it is playing with fire. Even if the administration is reluctant to reduce this assistance, Congress may be less so, particularly in the current budget climate.

Whether the U.S. administration chooses to use military aid or another aspect of the relationship as leverage, it must demonstrate clearly to Egypt’s military the seriousness of the consequences of this crackdown on civil society. Last week in his speech before the United Nations General Assembly, President Obama reiterated that, “We will pursue a deeper engagement with governments, but also with civil society – students and entrepreneurs, political parties and the press … and we will always serve as a voice for those who’ve been silenced.” Now, as the Egyptian military does its best to silence Egypt’s civil society organizations, the administration should go beyond engagement with these groups to unequivocally stand up for their rights.